More than 80% of children who are killed or seriously injured as a result of abuse or neglect are missed by the national child protection register, the Guardian can reveal.

In the week that social workers from Haringey in London were lambasted over the horrific killing of a 17-month-old known as Baby P, and Manchester social services staff faced questions over the deaths of three-month-old Delayno Mullings-Sewell and his two-year-old brother, Romario, the findings show that scores of children who die at the hands of relatives are not on the radar of social services departments, even though in some cases injured babies have had medical treatment.

The figures, obtained from unpublished government-commissioned research, show a widespread pattern of missed opportunities where police, social workers and health professionals fail to communicate or act on evidence of potential abuse. Postmortem case reviews included in the research where children died in the care of their families reveal that midwives, hospital staff and social workers saw evidence of abuse while the children were still alive but councils did not place them on the child protection register.

Despite signs of the abuse being clear to authorities, infants who died from forced starvation, broken ribs and smashed skulls were all missed off the register, which lists 29,200 children "known to be suffering harm". Just 33 of the 189 children whose death or serious injury prompted a local authority serious case review between 2005 and 2007 were on the register, according to the analysis of the most serious cases to be submitted to ministers next spring.

The research has raised concerns that, across the country, procedures that should result in children at risk being protected by the government's flagship anti-child-abuse system are not being followed, leading to deaths that could be avoided. The number of serious cases in the period 2005-2007 rose 17% on the previous two years.

Concerns about the state of child protection have been exposed after the case of Baby P sparked furious clashes in the Commons and triggered two separate government inquiries, one to examine social services in Haringey, the other to revisit the national system established after the case of Victoria Climbié, who was murdered in the same north London borough eight years ago.

Yesterday at the Old Bailey the three people convicted of involvement in the Baby P case were warned that they face substantial jail terms.

Marion Brandon, a University of East Anglia academic who is leading the analysis of serious case reviews, said social workers often struggled to respond appropriately because they found cases frightening and confusing. "They make an early assessment, and don't tend to change their minds," she said. "They keep looking for evidence that supports their view and that can be very dangerous. They might stick to saying it is a case of neglect when it is actually abuse."

Between 2003 and 2005, 45% of children who were killed or seriously injured through abuse or neglect were not known in any way by the social services but may have been on the radar of other public authorities. "In cases where the authorities saw evidence that a child may have been abused, an investigation should have taken place which could result in the child being placed on the register," said Sally Trench, an independent social work consultant who works with local authorities. "There will inevitably be a number of neglected and abused children we don't know about, and I feel particularly concerned about babies and toddlers, who may rarely be seen by any professionals."

Between 2005 and 2007, the majority of serious cases involved a baby under the age of one. In most of those cases, they were younger than six months old. Almost a quarter of cases involved children over 11, with a significant minority aged between 16 and 18. These included suicides, sometimes following a history of abuse, missing persons and some teenagers who were victims of violence from non-family members.

"There are two peaks of vulnerability and danger - babies and older teenagers," said Brandon. "The smallest number we have found is between the ages of six and 10 which is the age bracket of Victoria Climbié [who died aged eight] and it was the inquiry into her death which has led to most of the recent learning. Our attention may have been deflected from the greater risks that we know are posed to babies. Since health visitors and midwives routinely work with babies they need to work more closely with social workers so that together they can offer better protection to these very young and potentially vulnerable children."

This month it emerged that three-year-old Tiffany Wright was starved to death in a room above a Sheffield pub despite concern being raised by a midwife and pub regulars. She was not on the child protection register and was found dead from bronchopneumonia and covered in insect bites.

In another case, Jessica Randall, from Kettering, lived for just two months and was referred to hospital several times, at least once with bruising. Her parents were known to social workers, but she was not on the child protection register either. She eventually died from a "massive skull fracture with subdural bleed" and her ribs had been broken.

Councils denied they were being negligent by missing similar cases off the register. "Quite a proportion of those deaths and serious injuries are unpremeditated and appear to come out of the blue," said Colin Green, director of children's services at Coventry city council speaking on behalf of the Association of Directors of Children's Services. "The parent may suffer an acute psychotic episode or there could be an adult suicide which is preceded by the murder of the children. It would have been extremely difficult to discern any threat to children in those cases."

He said the register was considered a "draconian intervention in family life" and that while some children may display bruises or other signs of harm, investigations could be inconclusive. "Judgments need to be made and they are not always going to be right," he said.

According to the most recent mortality statistics, 84 boys and 64 girls under the age of five died in 2006 from "injuries, poisoning and certain other consequences of external causes".

The causes of death in 38 cases were injuries to the head and neck including fatal fractures of the skull and facial bones and injuries to the thorax. Thirteen infants died from "injuries involving multiple body regions", 15 from the "effects of a foreign body entering through a natural orifice" and 14 from a "foreign body in the respiratory tract". A further 18 died from asphyxiation.

A previous study of serious case reviews found that one in three families suffered a combination of domestic violence, mental illness and substance abuse. A third of cases showed evidence of poor living conditions. "We have to understand more about what makes these complicated families tick," Brandon said. "Until we do that, we won't be able to properly grapple with them."

Concern emerged this week that government policy has discouraged councils from decisive intervention in suspected cases of abuse and neglect. Ofsted, the government agency that rates local authority children and young people's services departments, docks marks if children remain on the register for more than two years. Child protection lawyers also believe a steep rise in legal fees associated with taking children into care is putting children at risk. In May the court fee for a local authority to bring such a case to court rose from around £100 to £2,225.